When a series of bomb attacks ripped through Muslim neighborhoods, mosques and shrines in India in recent years, suspicion fell firmly on a familiar culprit: Islamist terror. After each incident, scores of Indian Muslims were rounded up, and many were tortured. Confessions were extracted, the names of various militant “masterminds” leaked to the media and links with Pakistan widely alleged.

Never mind that most of the victims were Muslims; it seemed natural to many people, from New Delhi to Washington, to assume the attacks were the work of extremist Pakistani militants and their Indian Muslim sympathizers, intent on fanning religious tensions in India and disrupting the peace process between the nuclear-armed rivals.

But those investigations, and the assumptions behind them, were turned on their head early this year by the confession of a Hindu holy man. Swami Aseemanand told a magistrate that the bomb makers were neither Pakistani nor Muslim but Hindu radicals, bent on revenge for many earlier acts of terrorism across India that had been perpetrated by Muslims.

His statement, subsequently leaked to the media, alleged that a network of radicals stretched right up to senior levels of the country’s Hindu nationalist right wing. It also exposed deep-seated prejudices within the police against the country’s minority Muslim population.

Ironically, the charges may also have helped India and Pakistan to get back to the negotiating table last month after relations broke down in the wake of the 2008 attacks on Mumbai.

A string of attacks

Like many Indians, Aseemanand was furious with terrorist attacks in the country carried out by Muslims. “We should answer bombs with bombs,” he told a small group of Hindu extremists in June 2006, only to discover a plot was already well under way.

In the ensuing 18 months, bombs were placed on bicycles in a Muslim cemetery in the western town of Malegaon, hidden under a granite slab in a mosque in Hyderabad and left in a tiffin lunchbox in an important Sufi shrine in Ajmer, all targets Aseemanand said he suggested.

In another attack, 68 people, most of them Pakistanis, were killed when suitcases packed with explosives were placed next to gasoline bottles on a train headed from western India to Pakistan. Many of the victims were unable to escape the inferno because of bars on the train windows, and their bodies were burned beyond recognition.

Evidence that radical Hindus, including an army colonel who is suspected of supplying the technical expertise and the explosives, were behind several of these bombings began to surface more than two years ago, and several people were arrested, including Aseemanand.

But his statement is the first clear evidence that Indian Hindu terrorists were to blame for the deaths of Pakistani Muslim travelers on the Samjhauta, or Friendship, Express.

Pakistan reacted to the news with ill-disguised glee, arguing that the botched investigations and the subsequent confession confirmed its suspicions that India “lacked the courage” to prosecute radical Hindus.

In India, there was sober reflection in some quarters about prejudices against Muslims. The Hindu right’s old adage, that “while not every Muslim is a terrorist, every terrorist is a Muslim,” could no longer be trotted out with a straight face.

India had been insisting it would not restart a formal peace process with Pakistan until that country properly investigated and prosecuted state-sponsored militants blamed for the attacks on Mumbai, which left 166 people dead.

Pakistan responded in kind, demanding a fuller and faster investigation into the train attack. India put on a brave face, but the revelations were an embarrassment, one official privately admitted, as Indian media judged that their government had lost some of the moral high ground.

The fallout

In a sense, though, the episode provided the political cover at home for Indian Prime Minister Manmohan Singh to agree this month to do what he secretly wanted and restart the peace process with Pakistan, said Commodore Uday Bhaskar of the National Maritime Foundation, a New Delhi think tank.

“Before, terrorism was projected in public opinion in black-and-white terms, that all terrorism was because of Muslims and because of Pakistan,” he said. Aseemanand’s confession “had an unintended positive kind of fallout and introduced a malleability into the India-Pakistan interaction.”

More damaging were Aseemanand’s accusations against high-ranking members of the Rashtriya Swayamsevak Sangh, or RSS, a religious group that spreads its Hindu revivalist ideology, known as Hindutva, through a network of schools, charities and clubs.

The RSS, the ideological parent of the country’s main opposition Bharatiya Janata Party, is also engaged in a sometimes violent contest with Christian missionary groups operating in India.

According to Aseemanand, the main organizer of the attacks was an RSS worker called Sunil Joshi, in his mid-30s, from the town of Dewas in the central Indian state of Madhya Pradesh.

Relatives describe Joshi as a conservative and deeply religious man of very few words, who spent most of his time in an ashram and visited the family only rarely. Nicknamed “monkey” by his older brother for his devotion to Lord Hanuman, Hinduism’s mighty ape god, Joshi viewed Muslims as “worthless,” his niece said.

Mysteriously, in late December 2007, after most of the bomb attacks had taken place, Joshi was gunned down in the street near his family home. Police think Joshi’s gang turned on him, but some investigators and family members believe he was killed because he was about to turn himself in to the police.

RSS national executive member Indresh Kumar, who is suspected of mentoring and financing the bomb-making gang, said in an interview that the accusations against him represented a “deep political conspiracy” by the ruling Congress party to defame him and the RSS.

Certainly, some members of the secular Congress party have enjoyed and exploited the Hindu nationalist opposition’s discomfort over the allegations. Rahul Gandhi, a leading member of Parliament and heir apparent to the Nehru-Gandhi dynasty, even told the U.S. ambassador in 2009 that radicalized Hindu groups were a bigger threat to India than support for Lashkar-i-Taiba, a militant group that is accused in the Mumbai attacks, according to a cable released by WikiLeaks.

Gandhi was widely criticized for that assertion, but the RSS has found itself on the defensive. In a series of conversations with The Washington Post, the group’s leaders portrayed the bomb makers as either paid agents of Pakistani military intelligence or simply as a violent splinter group of their peaceful movement.

Ajai Sahni, a terrorism expert who runs the Institute for Conflict Management in New Delhi, said the militants were just “the fringe of a fringe” within the Hindu right. But “the sympathies may be deeper within the core of Hindutva,” he said.

Muslims still in jail

Meanwhile, nine Muslims have languished in jail for more than four years, accused of carrying out the Malegaon bombings, in which 37 people were killed. They have been subjected, their attorney says, to horrific torture, their families reduced to poverty. But they hope Aseemanand’s confession will soon persuade a judge to release them on bail.

But Aseemanand’s attorney now says his client’s confession was obtained under duress and is not legally valid. In the confession, though, the holy man gave a different reason for wanting to come clean. In jail in Hyderabad, he apparently met a young Muslim named Kalim who was falsely accused of the bombing there and gradually warmed to him.

“I was very moved by Kaleem’s good conduct,” Aseemanand said. “My conscience asked me to do penance by making a confessional statement, so that the real culprits can be punished and no innocent has to suffer.”